Abstract Pneumonia caused by host-adapted, multiple drug resistant bacterial pathogens is a major clinical problem, associated with both primary infections and complications of hospitalization. Much of the pathology associated with these pathogens is due to the host response that is elicited ; either excessive inflammation that causes respiratory failure or an immunosuppressive response that permits unimpeded bacterial replication, pulmonary damage and sepsis. Organisms such as MRSA, Pseudomonas aeruginosa and Klebsiella pneumoniae readily adapt to the milieu within the human airways, acquiring mutations that affect their metabolism, immunogenicity as well as their resistance to antimicrobial agents. The goal of our studies is to apply a comprehensive approach to fully characterize such host adapted pathogens, isolated from patients, by using whole genome sequencing, murine modeling of immunogenicity, and proteomics. This type of analysis can provide the data necessary to identify bacterial components associated with specific patterns of infection. Bacterial genes that are linked to immuno-pathogenicity can be identified in clinical isolates in real time,just as methicillin resistance genes are routinely screened in staphylococci. A better understanding of the host response that is elicited will be used to apply immunomodulatory therapy to complement the often ineffective antimicrobial agents used to treat pneumonia. In other branches of medicine, targeting the inflammasome, IL-1, T cell signaling and TNF cascades have become standards of care and new immune targets are under active development. A comprehensive understanding of both the properties of the infecting organism and the host response that is evoked can be used to develop a strategy of precision medicine for the treatment of bacterial pneumonia.